Contacts of the helix formed by residues 307 - 318 (chain C) in PDB entry 2ATW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 307 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C ILE* 3.0 25.4 - - - -
304C GLY 2.6 15.5 + - - -
306C GLU* 1.3 72.7 - - - +
308C GLN* 1.3 54.5 + - - +
309C ASN 3.4 0.2 + - - -
310C ALA* 3.4 2.8 + - - +
311C ARG* 2.8 32.9 + - - +
7D A 3.7 2.6 - - - -
8D A 3.4 19.7 + - - -
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C GLU* 3.2 25.0 + - - +
216C HIS* 3.6 27.1 - - - +
217C ARG* 2.8 44.0 + - - +
303C ILE 3.3 1.6 + - - -
304C GLY* 3.8 1.2 + - - -
305C LYS* 3.3 18.3 + - + +
306C GLU 3.3 0.8 - - - -
307C GLY* 1.3 77.0 - - - +
309C ASN* 1.3 65.6 + - - +
311C ARG* 3.8 13.7 - - - +
312C LEU* 2.8 36.3 + - + +
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Residues in contact with ASN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ARG* 5.5 3.6 - - - +
219C LYS* 3.0 30.7 + - - +
256C ASP* 4.0 2.6 - - - +
272C LEU* 2.9 35.1 + - - +
273C SER 3.7 4.2 - - - +
274C PRO* 3.9 9.6 - - - +
275C ALA* 4.6 0.4 - - - +
301C LEU* 3.7 12.1 + - - +
302C ALA* 2.8 28.5 + - - +
303C ILE 3.0 6.2 + - - +
304C GLY* 4.0 4.6 - - - -
308C GLN* 1.3 81.4 - - - +
310C ALA* 1.3 57.4 + - - +
312C LEU* 4.9 0.4 - - - -
313C ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 4.2 9.2 - - - -
302C ALA 3.6 3.0 + - - -
303C ILE* 3.1 18.7 + - + +
307C GLY 3.8 5.6 - - - +
309C ASN* 1.3 77.0 - - - +
311C ARG* 1.3 56.8 + - - +
313C ALA* 3.2 1.9 + - - +
314C ALA* 2.8 31.4 + - - +
321C ILE* 4.0 4.4 - - + +
323C ILE* 4.3 7.0 - - + -
8D A 3.7 31.2 - - + +
10D A 4.0 10.9 + - - +
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C GLU* 2.7 43.9 + - - +
305C LYS 5.2 0.2 + - - -
306C GLU* 3.1 29.5 + - - +
307C GLY 2.8 23.5 + - - +
308C GLN* 3.7 16.6 - - - +
310C ALA* 1.3 71.9 - - - +
312C LEU* 1.3 59.2 + - - +
314C ALA* 3.2 3.1 + - - +
315C ARG* 2.9 39.9 + - - +
8D A 5.0 5.7 + - - -
10D A 3.6 38.3 + - + -
11D G 4.9 15.9 - - - -
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ALA* 3.6 22.9 - - + +
213C GLU* 3.5 27.1 - - + +
217C ARG* 3.5 45.3 - - + +
219C LYS* 3.6 23.6 - - + -
308C GLN* 2.8 32.2 + - + +
311C ARG* 1.3 74.6 - - - +
313C ALA* 1.3 62.5 + - - +
315C ARG* 3.2 21.4 + - - +
316C LEU* 2.8 31.0 + - - +
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Residues in contact with ALA 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C LYS* 3.7 7.9 - - - +
271C ALA* 3.6 32.3 - - + +
272C LEU* 3.9 10.3 - - + -
309C ASN 3.0 18.8 + - - +
310C ALA 3.6 4.0 - - - +
312C LEU* 1.3 78.0 - - - +
314C ALA* 1.3 58.1 + - - +
316C LEU* 3.2 1.4 + - - +
317C THR* 2.9 34.8 + - - +
321C ILE* 3.7 15.3 - - + -
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Residues in contact with ALA 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ALA 2.8 17.7 + - - +
311C ARG 3.5 4.0 - - - +
313C ALA* 1.3 77.6 - - - +
315C ARG* 1.3 57.3 + - - +
317C THR* 3.9 0.4 - - - -
318C GLY* 2.8 30.3 + - - -
319C TRP 3.2 23.2 + - - +
321C ILE* 3.4 7.1 - - + +
10D A 3.7 34.5 - - + +
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Residues in contact with ARG 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PRO* 5.8 4.2 - - - +
209C ALA* 5.8 0.2 - - - +
210C VAL 4.9 2.8 + - - +
211C ALA* 4.0 11.2 - - + +
212C ARG* 3.1 43.9 + - - +
213C GLU* 4.0 10.9 + - - +
311C ARG* 2.9 30.5 + - - +
312C LEU* 3.7 21.8 - - - +
314C ALA* 1.3 77.5 - - - +
316C LEU* 1.3 64.8 + - - +
318C GLY* 3.7 6.2 + - - -
10D A 3.9 17.3 - - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ALA* 3.5 51.7 - - + +
210C VAL 4.0 0.9 - - - -
211C ALA* 3.8 10.7 - - + +
219C LYS* 3.5 26.9 - - + +
221C ALA* 3.8 22.9 - - + +
258C ILE* 4.0 31.2 - - + -
267C PHE* 4.1 8.7 - - + -
271C ALA* 4.1 10.5 - - + -
312C LEU 2.8 18.1 + - - +
313C ALA* 3.5 5.6 - - - +
315C ARG* 1.3 81.8 - - - +
317C THR* 1.3 60.3 + - - +
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Residues in contact with THR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C PHE* 3.7 40.8 - - + +
268C VAL* 4.1 11.5 - - - +
271C ALA* 3.7 23.6 - - + -
288C ARG* 3.4 12.5 + - - -
313C ALA 2.9 16.8 + - - +
314C ALA* 3.5 2.8 + - - -
316C LEU* 1.3 76.2 - - - +
318C GLY* 1.3 60.1 + - - +
319C TRP* 3.0 36.1 + - - +
321C ILE* 4.3 1.1 - - + +
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Residues in contact with GLY 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ARG* 3.3 36.9 + - - +
314C ALA 2.8 13.1 + - - -
315C ARG* 3.7 5.3 + - - -
316C LEU 3.5 2.2 + - - -
317C THR* 1.3 77.0 - - - +
319C TRP* 1.3 61.8 + - - +
320C ARG* 4.3 0.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il